Structure of PDB 3qxt Chain B Binding Site BS01

Receptor Information

>3qxt Chain B (length=124) Species: 9844 (Lama glama)

QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAK
ISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADD
NYVTASWRSGPDYWGQGTQVTVSS

Ligand information

• Ligand ID: MTX
• InChI: InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
• InChIKey: FBOZXECLQNJBKD-ZDUSSCGKSA-N
• SMILES:
  CACTVS 3.341: CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
  CACTVS 3.341: CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
  OpenEye OEToolkits 1.5.0: CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
  ACDLabs 10.04: O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
  OpenEye OEToolkits 1.5.0: CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
• Formula: C20 H22 N8 O5
• Name: METHOTREXATE
• ChEMBL: CHEMBL34259
• DrugBank: DB00563
• ZINC: ZINC000001529323
• PDB chain: 3qxt Chain B Residue 2000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3qxt An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): V4 A26 R28 R29 S30 S31 R32 W34 M36 R74 N79 T80 V81 Y120
• Binding residue (residue number reindexed from 1): V2 A24 R26 R27 S28 S29 R30 W32 M34 R72 N77 T78 V79 Y113
• Annotation score: 1
• Binding affinity: MOAD: Kd=6700nM

External links

• PDB: RCSB:3qxt, PDBe:3qxt, PDBj:3qxt
• PDBsum: 3qxt
• PubMed: 21557375